Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years


Posted by Web Master (March 26, 2024)

New Mascot distributor in Europe: MS Wil B.V.

We are pleased to announce a new distributor for Matrix Science products!

Customers in Europe can now buy Mascot through MS Wil B.V., a one-stop-shop for fine mass spectrometry tools. MS Wil is selling new licences for Mascot Server and Mascot Distiller as well as updates and upgrades to existing licences.

The new distribution agreement means buying Mascot has never been easier: specify Mascot as part of your instrument package when buying through Bruker, Shimadzu, Thermo or Waters; order from MS Wil when stocking up on lab consumables; or buy direct from Matrix Science Ltd.

If you have an existing support contract, there is no change to your support status. Licences bought through European distributors and marketing partners continue to supported directly by Mascot developers based in the UK.

Posted by Web Master (January 30, 2024)

Obsolete IPI definitions and SARS-CoV-2 pre-release definition have been removed

Mascot Server ships with predefined configuration for several sequence databases, stored in databases_1.xml. The following definitions have become obsolete and have now been removed from databases_1.xml:

  • IPI_arabidopsis
  • IPI_bovine
  • IPI_chicken
  • IPI_human
  • IPI_mouse
  • IPI_rat
  • IPI_zebrafish
  • SARS-CoV-2

The International Protein Index (IPI) databases were superceded by Uniprot proteomes as long ago as September 2011. We kept the predefined definitions, because the FASTA files were still available at the EBI website. However, those files are no longer available, so there is no reason to keep these long-obsoleted definitions.

The SARS-CoV-2 predefined definition was added in March 2020, when Uniprot published a pre-release database for the virus. Since then, the sequences have been reviewed and incorporated in SwissProt, and in fact, the pre-release FASTA file disappeared from the Uniprot servers around September 2023. There is no reason to keep the SARS-CoV-2 definition – please use SwissProt instead, or set up a suitable Uniprot proteome database.

Removing the predefined definitions does not delete any databases in your local Mascot Server installation. If you had enabled any of the above, their local configuration points to the previous version of databases_1.xml and the sequence databases continue to work. The removal simply means you won’t be able to enable them on a new system or re-enable if you delete them. If you still need the databases, it’s best to make a copy in Database Manager and make sure it’s part of your backups.

Posted by Web Master (January 17, 2024)

Server upgrade

We have upgraded the server hardware and operating system, as well as migrated to a new hosting provider. The website and the free Mascot service should now operate normally. If you discover any issues, please contact us at

We have additionally moved searches older than 1 Jan 2020 to cold storage. If you submitted a search before 1 Jan 2020 and would like to download a copy, please send us an e-mail and we can send you the results file.

The server migration was originally scheduled for Saturday 20 January, with expected maximum downtime of 6 hours. The old server was meant to be running until the morning of 20 January, then switch over to the new server.

At about 16:15 UTC on Tuesday 16 January, we were finalising data migration and setting up the new server when the network connection to the old server was abruptly lost. Our previous hosting provider disconnected the IP feed without telling us. Because they could not provide any time estimate for restoring the IP feed, we accelerated the migration schedule to Wednesday 17 January. We apologise for the unplanned and extended downtime, which was due to actions outside our control.

If you submitted Mascot searches between 14 January 23:00 UTC and 16 January 16:15 UTC, your search results have not yet been copied to the new server. UPDATED on 18 Jan: We have now copied the 14-16 January searches to the new server. No data has been lost. Please e-mail us if you have any questions.

Posted by Web Master (October 5, 2023)

Mascot Distiller 2.8.5 patch release

Mascot Distiller 2.8.5 is a new patch release.

This release includes a number of important bug fixes, and we advise all users to download and install it.

Please do not hesitate to contact us with any questions.

Posted by Web Master (September 18, 2023)

Redesign of Mascot Distiller technical support pages

The Mascot Distiller technical support pages have been redesigned. The main page now lists the full version history, including links to related content like blog articles and Youtube videos. Each major version has its own page, like Distiller 2.8, which contains the list of known issues and the full change log for that major version. We hope this makes release information easier to find.

Posted by Web Master (September 5, 2023)

Moving searches older than 2015 to cold storage

When you submit a free search on the public Mascot server, the search results are stored on the server for a certain time, but we don’t guarantee they will be kept indefinitely. The size of the search archive has increased substantially since the limits were increased in March 2020. In order to avoid running out of storage space, we are gradually moving some of the historic archive into cold storage.

In November 2022, we archived search results up to 1 Jan 2010. On 5 September 2023, we have now moved all searches up to 1 Jan 2015 into cold storage. If you submitted a search before 1 Jan 2015 and would like to download a copy after the archival, please send us an e-mail and we can send you the results file.

The archival policy only affects Mascot running on our public website. If you have an in-house licence, the above policy does not apply.

Posted by Web Master (August 21, 2023)

Mascot Server 2.8.3 patch release

Mascot Server 2.8.3 has been released. This patch fixes six small bugs in the search engine (nph-mascot.exe), four in Mascot Perl scripts, one in ms-monitor.exe regarding a spurious log message and one issue with licensing on AMD EPYC processors.

We recommend all users to install the update. The cumulative update from 2.8.0, 2.8.1 and 2.8.2 can be downloaded from the support page.

  • 14038: Chimeric spectrum peaklist with some dodgy precursors causes Mascot to crash almost immediately
  • 14095: ShowSubSets in is probably broken in 2.8.1
  • 14105: Crash from chimeric spectra MGF when decoy selected
  • 14142: Scoring of N-terminal and C-terminal crosslinks occasionally too low, caused by fragment mass miscalculation when linking terminus to residue
  • 14189: Can’t call method “resetKeepAlive” on an undefined value at ./ line 667.
  • 14246: MaxConcurrentSearches not respected evenly on the master and the node
  • 14270: “Prepare ../taxonomy/acc_to_taxid.mapping.txt_*.cdb” even though nothing needs to be done
  • 14291: Disulfide crosslink search hangs at 67% due to number of open filehandles
  • 14340: Executable aborts immediately on AMD EPYC 7763 if creating an ms_processors object
  • 14366: xiView column CalcMz calculated using a hydrogen rather than a proton
  • 14367: Prevent PMF with Big Mascot
  • 14403: Peptide View reports C-terminal modification on wrong residue

Please do not hesitate to contact us with any questions.

Posted by Web Master (August 16, 2023)

New help page for chimeric spectra

We’ve added a new help page for chimeric spectra. Support for identifying peptides from chimeric spectra was added in Mascot Server 2.5 (2014) and Mascot Distiller 2.5 (2013), but it was not properly documented until now.